Baking animations on a Rigify rig with child of constraints does not preserve constraint
Ok, maybe this is not the best answer but it worked:
I duplicated the skeleton (just the deform bones from the original skeleton, NOT the rigify stuff). Then I added copy-transform constraints to all these new bones, mapping them back to the original.
Now on the new skeleton I can bake and everything works. I suspect the issue is that &quot;clear constraints&quot; does something that does not play nicely with Rigify, but am not sure. Duplicating to a new skeleton that copies the original worked.